# HG changeset patch
# User jcb-mpl
# Date 1652357494 0
# Node ID cfcdd499c781f9ffb877253c8dd583823964b1d0
# Parent  679024760b59669cc595cb5ab6e4ffd5b5234a23
Uploaded

diff -r 679024760b59 -r cfcdd499c781 eics_check_references.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eics_check_references.xml	Thu May 12 12:11:34 2022 +0000
@@ -0,0 +1,154 @@
+<tool id="2021_05_eics_check_references" name="EICs -> checks reference mz" version="0.0.1">
+  
+  <description> for 5 determined thresholds for m/z  </description>
+ 
+  <requirements>
+      <requirement type="package">scilab</requirement>
+  </requirements>
+  
+  
+  <stdio>
+      <exit_code range="1:" level="fatal" />
+  </stdio>
+  
+  
+  <command> <![CDATA[
+  $__root_dir__/packages/scilab-*/bin/scilab-cli -nb -quit -f ${script_file} 
+  ]]>
+  </command>
+
+
+  <configfiles>
+    <configfile name="script_file"> <![CDATA[ exec("$__tool_directory__/src/mz_0_publi_features4_galaxy.sci",-1); ...
+        exec("$__tool_directory__/src/mz_6bis_durbin_watson.sci",-1); ...
+        lasterror(); ...
+        ...
+        x_in=glx_tab2div("${xtrmz4}"); ...  // 20avril21
+        [x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}",x_in, ${electron}); ...
+        ... //[x_bilan,x_synthese,x_tr_mz4]=mz_0_publi_features4_galaxy("${mzref}", "${xtrmz4}", ${electron}); ...
+        ...
+        div2tab(x_bilan, "${xbilan}"); ...
+        save("${xsynthese}","x_synthese"); ...
+        save("${x_tr_mz_trouves}","x_tr_mz4"); ...
+        if ~isempty(lasterror(%f)); ...
+        write(0,lasterror()); ...
+        end; ]]>
+    </configfile>
+  </configfiles>
+
+ 
+  <inputs>
+    <param name="mzref"       format="tabular"            type="data"      label="Reference m/z values"    />
+    <param name="xtrmz4"      format="tabular"            type="data"      label="EICs-mean"    />
+    <param name="electron"    size="5"       value="0"    type="integer"   label="Electron mass" help="1=correction of the reference m/z values; 0=no correction"    />
+  </inputs>
+
+
+  <outputs>
+    <data name="xbilan"           format="tabular"      label="m/z check-summary"  />
+    <data name="xsynthese"        format="mat"          label="m/z check-details"  />
+    <data name="x_tr_mz_trouves"  format="mat"          label="m/z check-matrix"   />
+  </outputs>
+  
+  
+  <tests>
+  
+    <test>
+       <param  name="mzref"                 value="ref_mz.tab"/>
+       <param  name="xtrmz4"                value="EICs-merged.tab"/>
+       <output name="xbilan">
+           <assert_contents> 
+       	<has_text text="0.00034"/>
+       	<has_text text="0.352"/>   
+           </assert_contents>
+       </output>
+    </test>
+    
+  </tests>
+<help>
+
+
+**Author**  Jean-Claude Boulet (INRA).
+
+
+---------------------------------------------------
+
+=======================================================================
+CHECK REFERENCE MZ VALUES AMONG THE EICS-MEAN YIELDED BY THE PROCESSING
+=======================================================================
+
+-----------
+Description
+-----------
+
+A matrix of EICs has been yielded by the function: MS-centroid -> EICs-individual or by the function: several EICs-shared -> one EICs-mean.
+
+The m/z values of these EICs are compared to reference m/z values for 5 pre-determined threshold values for m/z: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100. 
+
+This function is focused on the m/z values, it does not take into account the retention times. 
+
+
+
+------
+Inputs
+------
+
+**reference m/z values**
+
+A tabular file, to the div format (first columns and rows = labels):
+
+- the first column corresponds to names of chemical compounds;
+
+- the second column contains the exact (reference) m/z values.
+
+
+**EICs-mean or individual**
+
+A tabular matrix of (RT x m/z); lines are retention times and columns are EICs.
+
+
+----------
+Parameters
+----------
+
+**correction of the electron mass**
+
+A correction can be applied to the reference m/z values. 
+
+- 0: no correction;
+
+- 1: correction = subtraction of 0.00055 in the positive mode. 
+
+
+
+------
+Output
+------
+
+**summary**
+
+The main results  
+
+
+**details**
+
+A .mat file
+
+
+**extracted EICs**
+
+An EIC is associated to a reference m/z value if the absolute difference of (EIC minus reference) is under a threshold. 
+
+Five threshold values have been pre-determined: 0.0005 / 0.0010 / 0.0030 / 0.0050 / 0.0100
+
+This output contains a list of 5 data, each containing the EICs identified as reference m/z values according to a threshold. 
+
+</help>
+
+
+<citations>
+
+</citations>
+
+
+</tool>